Retroviruses are major pathogens that can affect all vertebrates causing an extremely wide range of responses in infected animal hosts. For example, one of the most potent and lethal retroviruses is HIV-1, the agent that causes AIDS. Retroviruses are a large and diverse family of viruses that replicate by a unique process that is significantly different from other forms of viruses. The virion particles that make up retroviruses contain (+) strand genomic RNA. When the retrovirus enters a host cell, the (+) strand RNA is converted into double-stranded DNA through action of the enzyme reverse transcriptase (RT). This double-stranded DNA copy of the viral genome is called proviral DNA. The proviral DNA is then integrated into the host chromosomal DNA for replication by the action of the enzyme integrase (IN). Integration links the ends of linear proviral DNA to host genomic DNA. In a productive infection, proviral DNA acts as a template for the formation of retroviral particles and transcription of viral proteins, through the action of host RNA polymerase II. As integration of proviral DNA is necessary for replication, infected cells without integrated proviral DNA cannot spread infection. The formation of the integrated provirus is believed responsible for maintaining a persistent infection, for permanent entry into the host germ line and for mutagenic or oncogenic activities.
Current methods, licensed and approved by the FDA, for study of retroviruses such as HIV, include antibody-based assays, where antibodies are detected using ELISA (enzyme linked immunosorbent assay) or EIA (enzyme immunoassay) methods. PCR-based methods have also been used to study retroviruses. In these assays, DNA is detected by PCR amplification with virus-specific primers.